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feat: validate sequence #21

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feat: validate sequence #21

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12 changes: 10 additions & 2 deletions src/util.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -529,11 +529,19 @@ struct Record
meta :: String
end

name(r::Record) = isempty(r.meta) ? r.name : r.name * " " * r.meta
name(r::Record) = isempty(r.meta) ? r.name : r.name * " " * r.meta

NL = '\n'
Base.show(io::IO, rec::Record) = print(io, ">$(rec.name) $(rec.meta)$(NL)$(String(rec.seq[1:40]))...$(String(rec.seq[end-40:end]))")

function validate(dna::Array{UInt8})
if sum(wcpair[nuc+1] == 0 for nuc in dna) > 0
error("invalid sequence inside fasta")
end

return dna
end

"""
read_fasta(io::IO)

Expand All @@ -555,7 +563,7 @@ function read_fasta(io::IO)
write(buf,rstrip(line))
line=readline(io)
end
put!(chan, Record(take!(buf), name, meta))
put!(chan, Record(buf |> take! |> validate, name, meta))
end

close(buf)
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